Mac binaries

[jabaws.git] / website / archive / binaries / mac / src / globplot / biopython-1.50 / Bio / File.py

diff --git a/website/archive/binaries/mac/src/globplot/biopython-1.50/Bio/File.py b/website/archive/binaries/mac/src/globplot/biopython-1.50/Bio/File.py
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+# Copyright 1999 by Jeffrey Chang.  All rights reserved.
+# This code is part of the Biopython distribution and governed by its
+# license.  Please see the LICENSE file that should have been included
+# as part of this package.
+
+"""Code for more fancy file handles.
+
+
+Classes:
+UndoHandle     File object decorator with support for undo-like operations.
+StringHandle   Wraps a file object around a string.
+SGMLHandle     File object that automatically strips SGML tags from data.
+
+SGMLStripper   Object that strips SGML.  This is now considered OBSOLETE, and
+               is likely to be deprecated in a future release of Biopython,
+               and later removed.
+
+"""
+import os
+import StringIO
+import sgmllib
+
+class UndoHandle:
+    """A Python handle that adds functionality for saving lines.
+
+    Saves lines in a LIFO fashion.
+
+    Added methods:
+    saveline    Save a line to be returned next time.
+    peekline    Peek at the next line without consuming it.
+
+    """
+    def __init__(self, handle):
+        self._handle = handle
+        self._saved = []
+
+    def __iter__(self):
+        return self
+
+    def next(self):
+        next = self.readline()
+        if not next:
+            raise StopIteration
+        return next
+
+    def readlines(self, *args, **keywds):
+        lines = self._saved + self._handle.readlines(*args,**keywds)
+        self._saved = []
+        return lines
+
+    def readline(self, *args, **keywds):
+        if self._saved:
+            line = self._saved.pop(0)
+        else:
+            line = self._handle.readline(*args,**keywds)
+        return line
+
+    def read(self, size=-1):
+        if size == -1:
+            saved = "".join(self._saved)
+            self._saved[:] = []
+        else:
+            saved = ''
+            while size > 0 and self._saved:
+                if len(self._saved[0]) <= size:
+                    size = size - len(self._saved[0])
+                    saved = saved + self._saved.pop(0)
+                else:
+                    saved = saved + self._saved[0][:size]
+                    self._saved[0] = self._saved[0][size:]
+                    size = 0
+        return saved + self._handle.read(size)
+
+    def saveline(self, line):
+        if line:
+            self._saved = [line] + self._saved
+
+    def peekline(self):
+        if self._saved:
+            line = self._saved[0]
+        else:
+            line = self._handle.readline()
+            self.saveline(line)
+        return line
+
+    def tell(self):
+        lengths = map(len, self._saved)
+        sum = reduce(lambda x, y: x+y, lengths, 0)
+        return self._handle.tell() - sum
+
+    def seek(self, *args):
+        self._saved = []
+        self._handle.seek(*args)
+
+    def __getattr__(self, attr):
+        return getattr(self._handle, attr)
+
+    def __enter__(self):
+        return self
+
+    def __exit__(self, type, value, traceback):
+        self._handle.close()
+
+
+# I could make this faster by using cStringIO.
+# However, cStringIO (in v1.52) does not implement the
+# readlines method.
+StringHandle = StringIO.StringIO
+
+
+
+class SGMLHandle:
+    """A Python handle that automatically strips SGML tags from data (OBSOLETE).
+
+    This module is now considered to be obsolete, and is likely to be
+    deprecated in a future release of Biopython, and later removed.
+    """
+    def __init__(self, handle):
+        """SGMLStripper(handle)
+
+        handle is a file handle to SGML-formatted data.
+        
+        """
+        self._handle = handle
+        self._stripper = SGMLStripper()
+
+    def read(self, *args, **keywds):
+        data = self._handle.read(*args, **keywds)
+        return self._stripper.strip(data)
+
+    def readline(self, *args, **keywds):
+        line = self._handle.readline(*args, **keywds)
+        return self._stripper.strip(line)
+
+    def readlines(self, *args, **keywds):
+        lines = self._handle.readlines(*args, **keywds)
+        for i in range(len(lines)):
+            lines[i] = self._stripper.strip(str)
+        return lines
+
+    def __getattr__(self, attr):
+        return getattr(self._handle, attr)
+
+
+class SGMLStripper:
+    class MyParser(sgmllib.SGMLParser):
+        def __init__(self):
+            sgmllib.SGMLParser.__init__(self)
+            self.data = ''
+        def handle_data(self, data):
+            self.data = self.data + data
+
+    def __init__(self):
+        self._parser = SGMLStripper.MyParser()
+
+    def strip(self, str):
+        """S.strip(str) -> string
+
+        Strip the SGML tags from str.
+
+        """
+        if not str:  # empty string, don't do anything.
+            return ''
+        # I need to make sure that I don't return an empty string if
+        # the buffer is not empty.  This can happen if there's a newline
+        # character embedded within a tag.  Thus, I'll first check to
+        # see if the last character is a newline.  If it is, and it's stripped
+        # away, I'll add it back.
+        is_newline = str[-1] in ['\n', '\r']
+        
+        self._parser.data = ''    # clear the parser's data (don't reset)
+        self._parser.feed(str)
+        if self._parser.data:
+            str = self._parser.data
+        elif is_newline:
+            str = '\n'
+        else:
+            str = ''
+        return str
+